The Logan Square attack initially left the 18-year-old victim in a coma.
The two suspects, Terrance M. Ford, 15, of Chicago, and Aamwar W. Barbour, 16, of Oak Park, are both charged as adults. Barbour is a student at Oak Park-River Forest High School.
Both boys are charged as adults with kidnapping, robbery and aggravated sexual assault. Bond was set Tuesday at $750,000 for each defendant.
Prosecutors say surveillance video and witness statements place them at the scene and DNA evidence ties at least one of the teens to the assault.
A third suspect, allegedly involved in the attack, is still being sought by Chicago police.
Barbour's mother had no comment after the hearing, leaving her son's attorneys to assert his innocence.
"This is a young boy that's in high school," said Steven Pick, Barbour's attorney. "He's 16 years old. He was in class and got picked up by the police in class."
In court, prosecutors said Barbour and Ford allegedly raped and robbed the victim, an 18-year-old student at Highland Park High School.
Prosecutors say the victim was drunk that night and encountered the defendants at a restaurant near the Congress Theater after she was unable to get into a New Year's Eve concert there and became separated from her friends.
"The victim entered the restaurant and, due to her intoxicated state, fell down in the vestibule and sat herself against a wall," said Sean O'Callaghan, Cook County Asst. State's Attorney.
Prosecutors say Ford and Barbour brought the victim to their table where they were joined by six other people before surveillance cameras captured the entire group heading outside with the woman, who was unable to walk on her own. There on the corner Ford and Barbour allegedly fondled the victim and tried to take her purse.
"The defendants were confronted by an individual who told the defendants to stop what they were doing because the girl was intoxicated," said O'Callaghan. "The defendants, however, instead moved the victim."
Prosecutors say the woman fell and hit her head, causing it to bleed as the defendants carried the woman down a residential street. Ford then allegedly raped the victim on a patch of grass while others watched before witnesses nearby alerted Congress Theater security guards, who eventually detained the defendants.
Though prosecutors say blood on Ford's underwear matches the victim's DNA, Barbour's attorneys say no such evidence ties their client to the attack.
"There's six other kids that were talked about. We don't know who these other kids are. There is some video surveillance that might show our client is trying to help this victim," said Pick.
The third suspect who was not named in court has reportedly fled the state and is now being sought by police and federal authorities.
Ford and Barbour are being charged as adults but they are currently being held in juvenile detention.
Both teens have had run-ins with the law in the past, including theft and resisting arrest.